Genomics and epidemiology are used to track the spread of coronavirus in Victoria.

Epidemiology identifies how coronavirus is spreading using information about coronavirus and contact tracing. Contact tracing involves gathering information about someone who has coronavirus including when they developed symptoms, who they have been in contact with and the places they have been during the time when they are infectious.

We can also identify how coronavirus is spreading using genomics, where the genetic code of the virus is used to find which people with coronavirus have the same, or very similar, strains of the virus.

Used together, epidemiology and genomics can provide a better picture of how coronavirus has spread in Victoria.

How genomics is being used in Victoria

Coronavirus is made of RNA, which is a genetic code like DNA. Over time, very small changes happen to this code.

When someone tests positive for coronavirus, a sample of the virus is sent to the Victorian genomics public health laboratory at the Doherty Institute. The laboratory uses the sample to identify the code of the virus from that person. The codes from each sample of coronavirus are then compared to others. This allows us to find which samples have the same, or very similar, strains of the virus. A group of samples with the same or similar strain of coronavirus is known as a genomic cluster.

These results show how coronavirus is spreading through the community. It also provides information on how the virus is changing over time. This can also provide critical information about how coronavirus was introduced into a setting. By understanding how coronavirus is spreading in our community we can put in place measures that reduce the risk of coronavirus being introduced. An example of this is the new practices that have been introduced into meatworks to protect workers and prevent the spread of coronavirus.

Genomic analysis on its own cannot be used to identify who was the first case of coronavirus or who spread coronavirus to other people.

Genomics is not used to identify the DNA or genetics of a person who has coronavirus. The Department of Health and Human Services does not collect human DNA as part of coronavirus testing.

Victorian clusters

The Genomic diagram (PDF)  shows the genomic clusters of cases of coronavirus in Victoria. This diagram is being released to provide Victorians with more information about how coronavirus has spread in our communities.

  • Genomic clusters are identified when cases of coronavirus have similar RNA codes.
  • The left side of the diagram shows the different genomic clusters of the virus and bottom of the diagram shows the timeline of the cluster. The earliest cases in a cluster start on the left, and the most recent cases are on the right.
  • The colour of the dot shows how people caught coronavirus – this is based off the best available information at the time.

What this diagram tells us about outbreaks in Victoria

  • This diagram identifies cases linked to strains that originated from:
    • Cedar Meats (transmission network 1)
    • Rydges Hotel (transmission network 2)
    • Stamford Hotel (transmission network 3)
  • A genomic cluster is sometimes named after the place where the outbreak first occurred.  This name does not mean that every case in the genomic cluster was a part of that outbreak. As the virus spreads to different locations new outbreaks can occur. As the virus is very similar and part of the same genomic cluster the outbreaks at different locations can be linked.
  • You can also see where coronavirus strains have evolved over time, resulting in different genomic clusters. For example, the virus which started as the Rydges outbreak has evolved into 10 genomic clusters following a super spreading event.
  • Many clusters, especially during the first wave, have been linked to the introduction of a strain from someone who has travelled to Victoria from overseas. Many strains in travellers are not linked to any other known cases in Victoria. Where there are clusters, many are small, which means that most people who returned from overseas did not spread the virus to many other people.
  • You can see in the diagram where a cluster has been contained or stopped. The Cedar Meats labelled cluster is an example of this. A cluster stops when everyone who has that strain of coronavirus has isolated so they are no longer spreading coronavirus.
  • Almost all of the current cases in Victoria (where the sequence is known) are related to the Rydges Hotel cluster. This hotel was used to quarantine individuals returning from overseas. From the genomic and epidemiological data, we know that a family of four who returned from overseas and were quarantining within the hotel, were the first to become unwell in this genomic cluster. Because this family became unwell very shortly after arriving home, it is likely that they acquired infection overseas.
  • The Stamford Hotel cluster is the other source of current cases in Victoria. This hotel was also used for quarantine for individuals returning from overseas. From the genomic and epidemiological data, we know that three people who returned home to Australia and were quarantining within the hotel were the first to become unwell in this genomic cluster. It is likely then these people acquired coronavirus overseas. From 21 February to 14 August 2020 there are 110 cases associated with this genomic cluster.
  • Of the 5,395 samples of coronavirus that we had genomic data to 14 August, 3,594 are associated with the Rydges Hotel cluster and 110 are associated with the Stamford Hotel cluster.
  • More recent data indicates that for the 1,589 cases sequenced from cases with symptom onset from 14 July to 14 August, all but 12 were linked to Rydges. The other 12 cases are linked to the Stamford Hotel cluster. It is likely that 99% of current cases of Covid-19 in Victoria have arisen from the Rydges or Stamford Plaza hotels.

Does this show all the cases in Victoria?

Not every person with coronavirus in Victoria is represented on this diagram. There are several reasons for this:

  • Not everyone who has coronavirus gets tested. Some people who have coronavirus don’t have any symptoms or only have very mild symptoms and don’t realise they need to get tested.
  • For some people who test positive to coronavirus the sample of the virus might not be of good enough quality for the laboratory to identify the RNA code.
  • Where there are five or fewer cases linked or it is possible to identify someone from this information, the clusters have been grouped to protect the privacy of the individuals.
  • Not every case has been linked to a cluster. There are many reasons for this, but it is particularly common where an individual has returned from overseas and doesn’t pass coronavirus on to anyone else. In this situation only that person has that particular strain of coronavirus.
  • Because of high numbers of cases, some cases have not yet had samples tested for their RNA codes.
  • It takes some time to process the sequence, and recent viral strains may not yet appear on this analysis.